PALM2AKAP2

PALM2 and AKAP2 fusion

Basic information

Region (hg38): 9:109498324-110172512

Previous symbols: [ "PALM2-AKAP2" ]

Links

ENSG00000157654 ∙ NCBI:445815 ∙ OMIM:604582 ∙ HGNC:33529 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PALM2AKAP2 gene.

• Inborn genetic diseases (24 variants)
• not provided (14 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALM2AKAP2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense			23	2	5	30
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	6	9

Variants in PALM2AKAP2

This is a list of pathogenic ClinVar variants found in the PALM2AKAP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-109780523-A-G		not specified	Uncertain significance (Jan 26, 2023)
9-109867542-G-A		not specified	Uncertain significance (Aug 30, 2021)
9-109880564-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-109880593-G-A		not specified	Uncertain significance (Nov 06, 2023)
9-109880605-G-A		not specified	Uncertain significance (Oct 17, 2023)
9-109880656-A-G		not specified	Uncertain significance (Sep 20, 2023)
9-109923766-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-109925074-C-A		not specified	Uncertain significance (Jul 11, 2022)
9-109931981-G-A		not specified	Uncertain significance (Nov 18, 2022)
9-110015956-G-A		not specified	Uncertain significance (Jul 13, 2021)
9-110016004-G-A		not specified	Uncertain significance (Oct 13, 2023)
9-110016022-C-G		not specified	Likely benign (Oct 14, 2023)
9-110048735-TCCCCCGGAGTCTCCTGGA-T		not specified	Benign (Dec 31, 2019)
9-110048819-A-G			Likely benign (Jan 19, 2018)
9-110136169-G-T		Malignant tumor of prostate	Uncertain significance (-)
9-110136236-A-G		not specified	Uncertain significance (Jun 28, 2022)
9-110136296-C-T			Benign (Nov 03, 2017)
9-110136319-G-A		not specified	Uncertain significance (Sep 22, 2022)
9-110136321-T-C			Likely benign (Nov 03, 2017)
9-110136395-T-A		not specified	Uncertain significance (Jun 30, 2023)
9-110136397-C-T		not specified	Uncertain significance (Oct 27, 2021)
9-110136401-A-G		not specified	Uncertain significance (Jul 26, 2022)
9-110136407-A-G		not specified	Uncertain significance (Aug 08, 2023)
9-110136428-G-A			Benign (Dec 31, 2019)
9-110136458-A-G		not specified	Uncertain significance (Nov 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALM2AKAP2	protein_coding	protein_coding	ENST00000374530	11	392204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000607	1.00	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.225	601	617	0.974	0.0000341	7174
Missense in Polyphen		220	251.85	0.87353		3118
Synonymous	0.0972	259	261	0.992	0.0000161	2213
Loss of Function	4.11	16	46.1	0.347	0.00000247	534

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000199	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to regulatory subunit (RII) of protein kinase A. May be involved in establishing polarity in signaling systems or in integrating PKA-RII isoforms with downstream effectors to capture, amplify and focus diffuse, trans-cellular signals carried by cAMP (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.4

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.214
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: regulation of cell shape
• Cellular component: membrane